Free Response Questions

1. Explain how the endomembrane system regulates protein traffic and performs metabolic
functions in the cell. (15 points)

The endomembrane system is a group of membranes and organelles in eukaryotic cells that works
together to modify, package, and transport lipids and proteins. It includes a variety of organelles , such
as the nuclear envelope and lysosomes, and the endoplasmic reticulum and Golgi apparatus. Although
it's not technically inside the cell, the plasma membrane interacts with other endomembrane
organelles, and it's the site where secreted proteins are exported. The endoplasmic reticulum(ER)
plays a key role in the modification of proteins and synthesis of lipids. It consists of a network of
membranous tubules and flattened sacs. The discs and tubules of the ER are hollow, and the space
inside is called lumen. The rough ER gets its name from the bumpy ribosomes attached to its
cytoplasmic surface. As these ribosomes make proteins, they feed the newly forming protein chains
into lumen. Some are transferred fully into the ER and float inside, while others are anchored in the
membrane. Inside the ER, the proteins fold and undergo modifications. These modified proteins will
be incorporated into cellular membranes or secreted from the cell. If the modified proteins are not
destined to stay in the ER, they will be packaged into vesicles and shipped to the Golgi apparatus. The
rough ER also makes phospholipids for other cellular membranes, which are transported when the
vesicle forms. The smooth ER is continuous with the rough ER but has a few or no ribosomes on its
cytoplasmic surface. The functions of the smooth ER include the synthesis of carbohydrates, lipids,
and steroid hormones, detoxification of medications and poisons, and storage of calcium ions. The
Golgi apparatus is an organelle made up of flattened discs of membrane. The receiving side of the
Golgi apparatus is called the cis face and the opposite is called the trans face. Transport vesicles from
the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi
apparatus. As proteins and lipids travel through the Golgi, they undergo further modifications. Finally
after the modified proteins are sorted and packaged into vesicles that bud from the trans face of the
Golgi. Some of these vesicles deliver their contents to other parts of the cell where they will be used.
Others fuse with the membrane, delivering membrane-anchored proteins that function there and
releasing secreted proteins outside the cell. Cells that secrete many proteins have many Golgi stacks.
In plant cells, the Golgi apparatus also makes polysaccharides. The lysosome is an organelle that
contains digestive enzymes and acts as the organelle-recycling facility of an animal cell. It breaks
down old and unnecessary structures so their molecules can be reused. Lysosomes are part of the
endomembrane system, and some vesicles that leave the Golgi are bound for the lysosome.
Lysosomes carry out intracellular digestion in a variety of circumstances. Amoebas and many other
unicellular eukaryotes eat by engulfing smaller organisms or food particles, a process called
phagocytosis. Lysosomes also use their hydrolytic enzymes to recycle the cell's own organic material,
a process called autophagy. Plant cells are unique because they have a lysosome-like organelle called
the vacuole. The large central vacuole stores water and wastes, isolates hazardous materials, and has
enzymes that can break down macromolecules and cellular components, like those of a lysosome.
Plant vacuoles also function in water balance and may be used to store compounds such as toxins and
pigments.

2. Explain the aerobic respiration of eukaryotic cells. (15 points)

Glycolysis releases less than a quarter of the chemical energy in glucose that can be harvested by
cells; most of the energy remains stockpiled in the two molecules of pyruvate. If molecular oxygen is
present in the eukaryotic cells, pyruvate enters the mitochondrion, where enzymes of the citric acid
cycle complete the oxidation of the organic fuel to carbon dioxide. After pyruvate enters the
mitochondria via active transport, it is converted to a compound called acetyl coenzyme A (or) acetyl
CoA. This step, linking glycolysis and the citric acid cycle, is carried out by a multienzyme complex
that catalyzes three reactions: (i) a carboxyl group is removed as CO2. The CO2 is fully oxidized and
thus has little chemical energy. (ii) The remaining two-carbon fragment is oxidized to form acetate.
An enzyme transfers the pair of electrons to NAD+ to form NADH. (iii) Acetate combines with
coenzyme A to form the very reactive molecule acetyl CoA. Due to the chemical nature of the CoA
group, a sulfur-containing compound derived from a B vitamin, acetyl CoA has a high potential
energy. Acetyl CoA now feeds its acetyl group into the citric acid cycle for further oxidation. The
citric acid cycle is also called the tricarboxylic acid cycle or the Krebs cycle. The citric acid cycle
functions as a metabolic furnace that oxidizes fuel derived from pyruvate. Three CO2 molecules are
released, including one released during the conversion of pyruvate to acetyl CoA. The cycle generates
one ATP per turn by substrate-level phosphorylation. Most of the chemical energy is transferred to
NAD+ and a related electron carrier, the coenzyme FAD, during the redox reactions. The reduced
coenzymes, NADH and FADH2, transfer high-energy electrons to the electron transport chain. The
citric cycle has eight steps, each catalyzed by a specific enzyme. In the cells of plants, bacteria, and
some animal tissues, the citric acid cycle forms an ATP molecule by substrate-level phosphorylation.
In many animal tissues, guanosine triphosphate is formed by the same process of substrate-level
phosphorylation. Most of the ATP produced by respiration results from oxidative phosphorylation,
when the NADH and FADH2 produced by the citric acid cycle relay the electrons from food to the
electron transport chain. This process supplies the necessary energy for the phosphorylation of ADP to
ATP.

Only 4 of 38 ATP produced by the respiration of glucose are produced by substrate-level

phosphorylation: 2 net ATP from glycolysis and 2 ATP from the citric acid cycle. NADH and FADH2
account for most of the energy extracted from glucose. The electron transport chain is a collection of
molecules embedded in the cristae, the folded inner membrane of the mitochondria. The folding of the
inner membrane to form cristae increases its surface acres, providing space for thousands of copies of
the chain in each mitochondrion. Electrons drop in free energy as they pass down the electron
transport chain. During the transport along the chain, electrons carriers alternate between reduced and
oxidized states as they accept and donate electrons. Electrons carried by NADH are transferred to the
first molecule in the chain, a flavoprotein. In the next redox reaction, the flavoprotein returns to its
oxidized form as it passes electrons to an iron-sulfur protein. The iron-sulfur protein then passes the
electrons to a compound ubiquinone. Most of the remaining electron carriers between ubiquinone and
oxygen are proteins called cytochromes. The last cytochrome of the chain, cyt a3, passes its electrons
to oxygen, which is very electronegative. The electrons carried by FADH2 have lower free energy and
are added at a lower energy level than those carried by NADH. The electron transport chain generates
no ATP directly. Its function is to break the large free-energy drop from food to oxygen into a series
of smaller steps that release energy in manageable amounts. A protein complex in the cristae, ATP
synthase, actually makes ATP from ADP and inorganic phosphate. ATP synthase works like an ion
pumping running in reverse. Enzymes can catalyze a reaction in either direction, depending on the ∆G
for the reaction, which is affected by the local concentrations of reactants and products. Rather than
hydrolyzing ATP to pump protons against their concentration gradient, ATP synthase uses the energy
of an existing ion gradient to power ATP synthesis. This process, in which energy stored in the form
of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of
 ATP, is called chemiosmosis. ATP synthase is a multisubunit complex with four main parts, each
made up of multiple polypeptides. ATP synthase molecules are the only place where H+ can diffuse
back to the matrix.The exergonic flow of H+ is used by the enzyme to generate ATP. This coupling of
the redox reactions of the electron transport chain to ATP synthesis is an example of chemiosmosis.
Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient
across a membrane to drive cellular work. In mitochondria, the energy for proton gradient formation
comes from exergonic redox reactions, and ATP synthesis is the work performed. During cellular
respiration, most energy flows as follows: glucose, NADH, electron, transport chain, proton-motive
force, ATP. The three main departments of this metabolic enterprise are glycolysis, pyruvate oxidation
and the citric acid cycle, and the electron transport chain, which drives oxidative phosphorylation.

3. Explain the photosynthesis of green plants. (15 points)

Photosynthetic enzymes and other molecules are grouped together in a biological membrane, allowing
the necessary series of chemical reactions to be carried out efficiently. The process of photosynthesis
likely originated in a group of bacteria with infolded regions of the plasma membrane containing
clusters of such molecules. All green parts of a plant have chloroplasts, but leaves are the major sites
of photosynthesis for most plants. Chloroplasts are found mainly in cells of mesophyll, the tissue in
the interior of the leaf. O2 exits and CO2 enters the leaf through microscopic pores called stomata in
the leaf. Veins deliver water from the roots and carry off sugar from mesophyll cells to roots and
other nonphotosynthetic areas of the plant. A typical mesophyll cell has 30–40 chloroplasts, each
measuring about 2–4 µm by 4–7 µm. Each chloroplast has two membranes around a dense fluid
called the stroma. Suspended within the stroma is an internal membrane system of sacs, the
thylakoids. The interior of the thylakoids forms another compartment, the thylakoid space. Thylakoids
may be stacked in columns called grana. Chlorophyll, the green pigment in the chloroplasts, is located
in the thylakoid membranes. Chlorophyll plays an important role in the absorption of light energy
during photosynthesis. The photosynthetic membranes of prokaryotes arise from infolded regions of
the plasma membranes, also called thylakoid membranes. The equation describing the process of
photosynthesis is 6CO2 + 12H2O + light energy C6H12O6 + 6O2+ 6H2O → C6H12O6 is glucose,
although the direct product of photosynthesis is actually a three-carbon sugar that can be used to make
glucose. Water appears on both sides of the equation because 12 molecules of water are consumed
and 6 molecules are newly formed during photosynthesis. We can simplify the equation by showing
only the net consumption of water: 6CO2 + 6H2O + light energy → C6H12O6 + 6O2 Written this
way, the overall chemical change during photosynthesis is the reverse of cellular respiration. Both of
these metabolic processes occur in plant cells. However, chloroplasts do not synthesize sugars by
simply reversing the steps of respiration. In its simplest possible form, CO2 + H2O + light energy →
[CH2O] + O2, where [CH2O] represents the general formula for a carbohydrate. Both photosynthesis
and aerobic respiration involve redox reactions. During cellular respiration, energy is released from
sugar when electrons associated with hydrogen are transported by carriers to oxygen, forming water as
a by-product. The electrons lose potential energy as they “fall” down the electron transport chain
toward electronegative oxygen, and the mitochondrion harnesses that energy to synthesize ATP.
Photosynthesis reverses the direction of electron flow. Water is split and electrons are transferred
with H+ from water to CO2, reducing it to sugar. Because the electrons increase in potential energy
as they move from water to sugar, the process requires energy. The energy boost is provided by light.
Photosynthesis is two processes, each with multiple steps: light reactions and the Calvin cycle. The
light reactions (photo) convert solar energy to chemical energy. The Calvin cycle (synthesis) uses
 energy from the light reactions to incorporate CO2 from the atmosphere into sugar. In the light
reactions, water is split, providing a source of electrons and protons (H+ ions) and giving off O2 as a
by-product. Light absorbed by chlorophyll drives the transfer of electrons and hydrogen ions from
water to NADP+ (nicotinamide adenine dinucleotide phosphate), forming NADPH. The light
reactions also generate ATP using chemiosmosis, in a process called photophosphorylation. Thus,
light energy is initially converted to chemical energy in the form of two compounds: NADPH, a
source of electrons as reducing power that can be passed along to an electron acceptor, and ATP, the
energy currency of cells. The light reactions produce no sugar; that happens in the second stage of
photosynthesis, the Calvin cycle. The Calvin cycle is named for Melvin Calvin, who, with his
colleagues, worked out many of its steps in the 1940s. The cycle begins with the incorporation of
CO2 into organic molecules, a process known as carbon fixation. The fixed carbon is reduced with
electrons provided by NADPH. ATP from the light reactions also powers parts of the Calvin cycle.
Thus, it is the Calvin cycle that makes sugar, but only with the help of ATP and NADPH from the
light reactions. The metabolic steps of the Calvin cycle are sometimes referred to as light-independent
reactions because none of the steps requires light directly. Nevertheless, the Calvin cycle in most
plants occurs during daylight because that is when the light reactions can provide the NADPH and
ATP the Calvin cycle requires. In essence, the chloroplast uses light energy to make sugar by
coordinating the two stages of photosynthesis. Whereas the light reactions occur at the thylakoids, the
Calvin cycle occurs in the stroma. In the thylakoids, molecules of NADP+ and ADP pick up electrons
and phosphate, respectively, and NADPH and ATP are then released to the stroma, where they play
crucial roles in the Calvin cycle.

4. Explain the three stages of cell signaling. (15 points)

Reception is when a signaling molecule binds to a receptor protein and causes it to change shape. The
cell targeted by a particular chemical signal has a receptor protein on or in the target cell that
recognizes the signal molecule. Recognition occurs when the signal binds to a specific site on the
receptor that is complementary in shape to the signal. The signal molecule behaves as a ligand, a small
molecule that binds with specificity to a larger molecule. Ligand binding generally causes the
receptor protein to undergo a change in shape. Most signal receptors are plasma membrane proteins,
whose ligands are large, water-soluble molecules that are too large to cross the plasma membrane.
There are three major types of membrane receptors: G-protein-linked receptors, receptor tyrosine
kinases, and ion channel receptors. A G protein-coupled receptors (GPCRs) work with cytoplasmic G
proteins. Ligand binding activates the receptor, which then activates a specific G protein, which
activates yet another protein, thus propagating the signal. Receptor tyrosine kinases (RTKs) react to
the binding of signaling molecules by forming dimers and then adding phosphate groups to tyrosine
on the cytoplasmic part of the monomer making up the dimer. Relay protein can be activated by
binding to different phosphorylated tyrosine, allowing this receptor to trigger several pathways at
once. A ligand-gated ion channel opens to allow the flow of specific ions, such as Na+ or Ca2+,
through a channel in the receptor in response to binding by specific signaling molecules, regulating
the flow of specific ions across the membrane. The activity of all three types of receptors is crucial;
abnormal GPCRs and RTKs are associated with many human diseases. Intracellular receptors are
cytoplasmic or nuclear proteins. Signaling molecules that are hydrophobic or small enough to cross
the plasma membrane bind to these receptors inside the cell. At each step in a signal transduction
pathway, the signal is transduced into a different form, which commonly involves a shape change in a
protein. Many signal transduction pathways include phosphorylation cascades, in which a series of
protein kinases each add a phosphate group to the next one in line, activating it. Enzymes called
 protein phosphatases remove the phosphate groups. The balance between phosphorylation and
dephosphorylation regulates the activity of proteins involved in the sequential steps of a signal
transduction pathway. Second messengers, such as the small molecule cyclic AMP (cAMP) and the
ion Ca2+, diffuse readily through the cytosol and thus help broadcast signals quickly. Many G
proteins activate adenylyl cyclase, which makes cAMP from ATP. Cells use Ca2+ as a second
messenger in both GPCR and RTK pathways. The tyrosine kinase pathways can also involve two
other second messengers, diacylglycerol (DAG) and inositol trisphosphate (IP3). IP3 can trigger a
subsequent increase in Ca2+ levels. Some pathways lead to a nuclear response: Specific genes are
turned on or off by activated transcription factors. In others, the response involves cytoplasmic
regulation. Cellular responses are not simply on or off; they are regulated at many steps. Each protein
in a signaling pathway amplifies the signal by activating multiple copies of the next component; for
long pathways, the total amplification may be over a millionfold. The combination of proteins in a cell
confers specificity in the signals it detects and the responses it carries out. Scaffolding proteins
increase signaling efficiency. Pathway branching further helps the cell coordinate signals and
responses. Signal response is terminated quickly by the reversal of ligand binding.

5. (1) Describe the phases of mitosis in an animal cell. (8 points)

For convenience, mitosis is usually divided into five subphases: prophase, prometaphase, metaphase,
anaphase, and telophase. In late interphase, the chromosomes have been duplicated but are not
condensed. In prophase, the chromosomes are tightly coiled, with sister chromatids joined together.
The nucleoli disappear. The mitotic spindle begins to form. It is composed of centrosomes and the
microtubules that extend from them. The radial arrays of shorter microtubules that extend from the
centrosomes are called asters. The centrosomes move away from each other, apparently propelled by
lengthening microtubules. During prometaphase, the nuclear envelope fragments, and microtubules
from the spindle interact with the condensed chromosomes. Each of the two chromatids of a
chromosome has a kinetochore, a specialized protein structure located at the centromere. Kinetochore
microtubules from each pole attach to one of two kinetochores. Nonkinetochore microtubules interact
with those from opposite ends of the spindle. The spindle fibers push the sister chromatids until they
are all arranged at the metaphase plate, an imaginary plane equidistant from the poles, defining
metaphase. At anaphase, the centromeres divide, separating the sister chromatids. Each chromatid is
pulled toward the pole to which it is attached by spindle fibers. By the end, the two poles have
equivalent collections of chromosomes. At telophase, daughter nuclei begin to form at the two poles.
Nuclear envelopes arise from the fragments of the parent cell’s nuclear envelope and other portions of
the endomembrane system. The chromosomes become less tightly coiled.

(2) Explain how the eukaryotic cell cycle is regulated by a molecular control system. (7 points)

Signaling molecules present in the cytoplasm regulate progress through the cell cycle. The cell cycle
control system is molecularly based. Rhythmic fluctuations in the abundance and activity of cell cycle
control molecules pace the events of the cell cycle. These regulatory molecules are mainly proteins of
two types: protein kinases and cyclins. Protein kinases are enzymes that activate or inactivate other
proteins by phosphorylating them. Particular protein kinases give the go-ahead signals at the G1 and
G2 checkpoints. The kinases that drive the cell cycle are present at constant concentrations but require
the attachment of a second protein, a cyclin, to become activated. Levels of cyclin proteins fluctuate
cyclically. Because of the requirement for binding of a cyclin, the kinases are called cyclin-dependent
kinases, or Cdks. Peaks in the activity of one cyclin-Cdk complex, MPF, correspond to peaks in
cyclin concentration. Cyclin level rises sharply during the S and G2 phases and then falls abruptly
during mitosis. MPF (“maturation-promoting factor” or “M-phase-promoting factor”) triggers the
cell’s passage past the G2 checkpoint to the M phase.MPF triggers the breakdown of cyclin, reducing
cyclin and MPF levels during mitosis and inactivating MPF. The noncyclic part of MPF, the Cdk,
persists in the cell in inactive form until it associates with new cyclin molecules synthesized during
the S and G2 phases of the next round of the cycle. At least three Cdk proteins and several cyclins
regulate the key G1 checkpoint. Fluctuating activities of different cyclin-Cdk complexes are of major
importance in controlling all the stages of the cell cycle. Cyclic changes in regulatory proteins work
as a cell cycle clock. The key molecules are cyclins and cyclin-dependent kinases (Cdks). The clock
has specific checkpoints where the cell cycle stops until a go-ahead signal is received; important
checkpoints occur in G1, G2, and M phases. Cell culture has enabled researchers to study the
molecular details of cell division. Both internal signals and external signals control the cell cycle
checkpoints via signal transduction pathways. Most cells exhibit density-dependent inhibition of cell
division as well as anchorage dependence. Cancer cells elude normal cell cycle regulation and divide
unchecked, forming tumors. Malignant tumors invade nearby tissues and can undergo metastasis,
exporting cancer cells to other sites, where they may form secondary tumors. Recent cell cycle and
cell signaling research, and new techniques for sequencing DNA, have led to improved cancer
treatments.