Download Exam #2 Review

Exam #2 Review
Exam #2 will cover all the material that has been presented in class since Exam #1
and up through the metabolism introduction. This includes eukaryotic cell
structure / function, transport, the closed system growth curve, enzymes and the
introduction to metabolism. As always, it is best to begin by studying your notes
and then after you feel your study is complete, take some time to look through this
review.
I. Eukaryotic cell structure / function
A. There is a great deal of variance among eukaryotic cells - from protozoan
cells to yeast cells to human cells. Fungi and protists (classically split into
algae and protozoa) are eukaryotic representatives of the microbial world.
B. Structure of the eukaryotic cell.
1. Cytoskeleton - provides structure and shape of cell, three
components:
a. Microtubules - largest element of cytoskeleton, composed of
hollow cylinders of tubulin, form mitotic spindles, cilia and
flagella and cell “highways”.
b. Microfilaments - smallest element of cytoskeleton,
composed of actin, involved in motion (pseudopod formation).
c. Intermediate filaments - very stable structural element, play
a supportive role, composed of proteins including keratin.
Practice: Microfilaments
a. are a component of the cytoskeleton.
b. are long, twisted polymers of a protein called actin.
c. form eukaryotic flagella.
d. are made of tubulin.
e. a and b
f. c and d
2. Nucleus
a. Bound by both an inner and outer membrane. The space
between the two membranes is called the perinuclear space. The
membrane has large nuclear pores through which proteins can
pass (Why is this important?)
b. Linear pieces of DNA are packaged by wrapping one and
three quarters times around a histone octamer to form a core
particle. Neighboring core particles are linked by DNA. This
linker DNA associates with another histone called H1.
Together, the core particle, H1 and some of the linker DNA
form a nucleosome. Histones are rich in what type of amino
acid? How does the charge of DNA / histones affect this
packaging process? Chromatin is the complex of DNA and
proteins that together form the chromosomes. How does
euchromatin differ from heterochromatin?
c. A region within the nucleus, called the nucleolus, is the site
of ribosome assembly.
Practice: The nucleus
a. is a double membrane sac containing DNA as is
found in eukaryotes.
b. Is a single phospholipid membrane sac
containing prokaryotic DNA.
c. is a smaller structure contained within the
eukaryotic nucleolus.
d. cannot transport molecules to the cytoplasm due
to the double membrane barrier.
3. The Endoplasmic Reticulum
a. Rough ER - Site of synthesis of proteins targeted for the
membrane, for secretion or for specific organelles. (Studded
with 80S ribosomes (*60S and 40S subunits))
What is the medical importance of the fact that prokaryotes
have 70S ribosomes and eukaryotes 80S?
b. Smooth ER - Site of lipid and steroid hormone synthesis,
location of calcium ion storage. (No ribosomes cover the
surface, thus smooth).
*vesicles bud off of both of these organelles carrying the
recently synthesized compounds. These vesicles are targeted
for the Golgi.
Practice: Which one of the following would be the site of
synthesis and folding, but not final modification of a protein
needed outside the cell?
a. The Golgi apparatus
b. The mitochondria
c. The smooth ER
d. The rough ER
4. The Golgi apparatus - molecules from ER are further modified
(e.g. addition of carbohydrate or phosphate groups). Vesicles bud off
of Golgi and carry modified molecules to their destination. The Golgi
has a cis and a trans face that differ substantially from one another.
Practice: The Golgi Apparatus
a. is the site of modification of molecules from the ER.
b. has an acidic pH and is filled with hydrolytic, digestive
enzymes.
c. is found exclusively in plants and algae.
d. is considered the “powerhouse” of the eukaryotic cell.
e. both b and c
5. Lysosomes - acidic interior, filled with digestive enzymes to
hydrolyze macromolecules.
6. Mitochondria - powerhouses of the cell!
Practice - draw this organelle and label all parts. Where are the
components of the electron transport chain?
Practice - Which one of the following organelles contains its own
DNA genome and 70S ribosomes?
a. lysosomes
b. the endoplasmic reticulum
c. mitochondria
Which statement/s regarding mitochondria is/are FALSE?
a. Mitochondria are capable of converting CO2 into
organic compounds.
b. Mitochondria reproduce by binary fission.
c. Nearly all eukaryotic cells contain mitochondria.
d. Mitochondria contain their own DNA genome
7. Chloroplasts
Practice - draw this organelle and label all parts. Where are the
components of the electron transport chain?
Practice - Both chloroplasts and mitochondria synthesize ATP
using the electron transport chain, in what ways are these two
organelles different (in terms of the origin of the electrons that
fuel the electron transport chain)?
Practice: Which of the following explains the origin of
mitochondria and chloroplasts?
a. The Chemiosmotic Hypothesis
b. The Endosymbiont Theory
c. The Fluid Mosaic Model
d. Spontaneous generation
8. Plasma membrane
In many ways the plasma membrane of a eukaryotic cell is similar to
that of a prokaryotic cell (e.g Both are composed of a semipermeable
phospholipid bilayer (fluid-mosaic). Both contain transport proteins.
Practice - List the ways in which the plasma membrane of a
eukaryotic cell is different than that of a prokaryotic cell.
a. Endocytosis
1. phagocytosis - Used to engulf large particles - cell
sends out long extensions called pseudopods. These
surround debris and form a phagosome which fuses with
a lysosome to form a phagolysosome (often termed cell
eating).
2. pinocytosis
a.) Macropinocytosis
b.) Clathrin-dependent (Receptor mediated)
c.) caveolae-forming
Practice: Which statement/s is/are TRUE?
a. Phagocytosis and pinocytosis are both types of
endocytosis.
b. Receptor mediated (clathrin-dependent)
endocytosis is a type of pinocytosis.
c. During phagocytosis, a phagolysosome is
formed.
d. During caveolae-forming endocytosis, no
lysosome fusion occurs, thus many pathogens enter
cells this way.
e. all of the above
*Remember that many pathogens exploit endocytosis to
enter a host cell.
b. Exocytosis
9. Flagella and cilia
Practice: How are flagella different in prokaryotes and
eukaryotes?
All of the following are true of eukaryotic flagella EXCEPT
a. eukaryotic flagella are composed of 9 pairs of microtubule
doublets.
b. eukaryotic flagella sometimes have lateral hairs called
flimmer filaments.
c. eukaryotic flagella are composed of a basal body, a hook and
a filament.
d. eukaryotic flagella function in motility by wave-like motion
(base to the tip or tip to the base).
Cilia
a. are also called pili.
b. are also called fimbriae.
c. are shorter than flagella.
d. move in two phases.
e. a and b
f. c and d
*NOTE: It is a good test of understanding to compare features of
prokaryotic and eukaryotic cells.
Practice: Which statement does NOT correctly summarize a
difference between prokaryotic and eukaryotic cells?
a. The electron transport chain of aerobically respiring
prokaryotic and eukaryotic cells is found across the cytoplasmic
membrane.
b. Whereas prokaryotes generally have a single chromosome,
eukaryotes usually have more than 1 chromosome for the
storage of genetic material.
c. eukaryotic cells have a membrane-bound nucleus whereas
prokaryotic cells have only a gel-like mass called the nucleoid.
d. Whereas prokaryotic cells secrete enzymes to digest
macromolecules, eukaryotes generally bring in large molecules
via endocytosis.
Which of the following is useful in distinguishing between
prokaryotic and eukaryotic cells?
a. the presence / absence of peptidoglycan
b. the type of ribosomes used for the synthesis of proteins
c. the presence of membrane-delimited organelles within the
cytoplasm
d. all of the above
For the following 5 cell components, please determine whether
they are generally present:
a. only in prokaryotes
b. only in eukaryotes
c. only in bacteria
d. in both prokaryotes and eukaryotes
____16) Endoplasmic reticulum
____17) A single circular chromosome
____18) N-acetylmuramic acid (NAM)
____19) diaminopimelic acid
____20) flagella
V. Microbial nutrition and growth
A. Uptake of nutrients (transport)
The diagram below summarizes the types of transport covered. Use this to
review the differences / similarities of each type of transport.
Practice: Transporters using this type of transport require no energy
but become saturated at high substrate concentrations.
a. active transport
b. simple diffusion
c. facilitated diffusion
d. none of the above
*During what type of transport is a molecule modified as it is
transported?
B. Protein secretion - be familiar with the Sec-dependent pathway!
C. Bacterial cells reproduce via binary fission: a parent cell replicates its
DNA, elongates, a septum forms and eventually cleaves off two distinct
daughter cells. With this type of growth, the increase in cell numbers is
exponential.
Practice: If a single cell lands on an agar plate and begins to divide, how
many cells will there be after the tenth cycle of division?
D. A researcher may also be interested in calculating the number of cells in a
population of cells that originated from more than a single cell.
The following equation can be used for this purpose and will be provided on
the exam:
N t = N o X 2n
where Nt = the # of cells in a population after a given time
No = The original number of cells in a population
n = the number of cycles of division (depends on doubling time)
Practice: 100 cells of Vibrio fischeri are used to inoculate a large bottle
of sterile media. If this bacteria has a doubling time of 2.5 h, how many
cells are present in the culture after an overnight incubation (16 h)?
C. In the lab, organisms are generally grown in closed (batch) systems (Why
are these systems called closed systems??). The Growth Curve describes
growth in closed systems. Please spend some time reviewing this growth
curve in your notes.
Practice: During which growth phase do cells begin to synthesize
secondary metabolites in response to increasing cell population
and buildup of waste products?
a. Lag phase
b. Initial log phase
c. Late log phase
d. Stationary phase
e. Death phase
Practice: (T or F) All of the cells in a culture die during the death
phase.
Practice: Which statement/s regarding the stationary phase of
growth is / are FALSE?
a. It is during the stationary phase that culture growth stops.
b. During the stationary phase, cells no longer synthesize any
metabolites.
c. The total number of viable cells stays constant during the
stationary phase.
d. Secondary metabolites are produced during the stationary phase.
e. it is during the stationary phase that cells are most sensitive to
antibiotics.
f. b and e
D. Why is growth in nature different from growth in a closed (batch)
system?
Nutritional Factors that Influence Microbial Growth (What do microbes need in
order to grow?)
*Revisit your crossword puzzle! Not covered extensively on the exam but very
important general knowledge to support your further learning. I will assume
knowledge of terms like chemoorganohetertroph, chemolithoatutroph,
psychrophile, acidophile etc.....
II. Enzymes
A. Catalyze reactions by lowering the reaction activation energy. Enzymes
lower the reaction activation energy by
1. holding the reactants in such a way that product formation is more
likely.
2. stabilizing the transition state (a transition state is a high-energy
complex that has a structure is somewhere between that of products
and reactants).
Practice: The following reaction curves both represent the same reaction,
which curve depicts the enzyme catalyzed reaction?
Enzymes have an active site at which they bind specifically to their substrate.
Enzymes either fit their substrate precisely (lock-and-key) or they change
their conformation slightly to fit the substrate = induced fit. After the
reaction has been catalyzed and the products are released, the enzyme
remains unchanged. Sometimes, two enzymes may recognize the same
substrate. What does this often lead to in a pathway?
B. Allosteric regulation - Some enzymes have another site, in addition to
the active site, called the allosteric site. An effector molecule binds to this
site, changes the shape of the enzyme and in doing so, either inhibits or
activates the enzyme. End products of many catabolic and anabolic pathways
serve as allosteric regulators for enzymes in the pathways that produce them
= feedback inhibition.
C. Some enzymes are regulated when a chemical group is covalently bound
to them. These enzymes are called interconvertible enzymes. In the
example in the notes, this interconvertible enzyme is active when it has a
phosphoryl group bound to it and inactive when it does not. The enzymes
that covalently modify interconvertible enzymes are called converter
enzymes. In the example in the notes, one converter enzyme acts to attach a
phosphoryl group (thus activating the interconvertible enzyme) and another
acts to remove that group (thus inactivating the interconvertible enzyme).
Pyruvate kinase (remember from step 10 of glycolysis) is an enzyme that is
extensively regulated by covalent modification.
C. Some enzymes can only function with the assistance of a cofactor. An
enzyme without its cofactor is termed an apoenzyme. When the enzyme has
its cofactor it is termed a holoenzyme. Apoenzymes are not active.
Cofactors are always non-protein components and can be split into two
groups: essential ions and coenzymes. Coenzymes can be further divided
into cosubstrates and prosthetic groups. Whereas cosubstrates can
dissociate from the enzyme (like NADH - that can dissociate and carry it’s
electrons to the ETC), prosthetic groups remain bound to the enzyme (like
FADH2 that can’t ever leave succinate dehydrogenase).
Practice: Coenzymes are derivatives of
a. minerals
b. proteins
c. lipids
d. vitamins
Practice: For her undergraduate research project a student is
studying a very active enzyme. The student notices that when she
treats the enzyme with a solution that removes metal ions, the
enzyme suddenly becomes inactive. Explain to the student why
this happens.
D. Enzymes can be inhibited either competitively or noncompetitively. In
competitive inhibition the inhibitor actually competes physically with the
substrate for access to the active site.
Practice: Which of the following is/are competitive enzyme
inhibitors?
a. sulfa drugs
b. Magnesium
c. NAD+
d. both a and b
e. both b and c
In noncompetitive inhibition, the inhibitor and substrate act at different
sites.
Competitive and noncompetitive inhibitors can inhibit either reversibly or
irreversibly. Irreversible inhibitors bind covalently and effectively “kill”
the enzyme. Penicillin is an example of an irreversible inhibitor. Reversible
inhibitors bind to an enzyme in such a way that the enzyme is unaltered.
III. Metabolism - overview
A. Catabolism = Harvesting energy released when a high-energy food
molecule is BROKEN DOWN (oxidized, degraded). Glycolysis and the
TCA cycle are basically catabolic pathways. However, because many of the
intermediates formed in these pathways can serve as precursor metabolites,
this gives these pathways a dual nature and we thus often call them
amphibolic pathways.
B. Anabolism = Energy (ATP) and reducing power (NADPH) are utilized to
BUILD (synthesize) complex molecules from simple building blocks (e.g.
the synthesis of amino acids).
Practice: Biosynthetic reactions that require energy for the
conversion of molecular subunits into larger molecules are called
a. kinetic energy
b. catabolic reactions
c. precursor molecules
d. anabolic reactions
Practice: Concerning catabolism and anabolism
a. they refer to reactions solely dealing with the
synthesis of lipids.
b. the intermediates of one serve as the reactants in
the other.
c. the energy gathered in one is utilized in the other.
d. they refer solely to the reactions involved in the
synthesis of proteins.
e. b and c
B. As can be seen by the definitions of catabolism and anabolism, ENERGY
is a central theme in metabolism. The processes are all about gaining and
utilizing energy.
1. Energy is never created or destroyed, it is simply converted from
one form to another = The First Law of Thermodynamics.
2. Because reactions are constantly taking place within a cell, the total
internal energy of that cell is constantly changing. The changes
observe the First Law of Thermodynamics in that if the cell looses
energy, the surroundings gains it and vise versa. The change in the
total internal energy of a cell is seen in the form of a heat transfer
which we represent as the change in enthalpy or ΔH. Is it more
favorable for a system (cell) to gain or loose heat?
3. In addition to heat transferred when a reaction takes place, the
nature of that reaction is also determined by The Second Law of
Thermodynamics which basically says that NATURE SEEKS
CHAOS. The entropy (S) of the universe is always increasing.
Is a negative or positive ΔS more favorable?
4. Thus, if a reaction is both releasing heat (ΔH is negative) and
undergoing an increase in disorder (ΔS is positive), the reaction is
spontaneous and exergonic (ΔG (free energy) is negative). A
reaction may be spontaneous and exergonic if there is a decrease in
disorder but the heat released must be great enough to make ΔG
negative. In the same way, a reaction may be spontaneous and
exergonic if heat is consumed as long as the increase in disorder still
allows ΔG to be negative.
ΔG = ΔH - TΔS
5. If ΔG is positive, the reaction is not spontaneous and is endergonic.
Practice: Exergonic reactions
a. occur when the value of ΔG is negative.
b. are spontaneous
c. occur when the value of ΔG is positive.
d. both a and b
e. both b and c
C. The First Law and the relationship between photoautotrophs and
chemoheterotrophs.
The relationship between photoautotrophs and chemoheterotrophs is all
about energy conversions and the First Law of Thermodynamics. Energy is
conserved when kinetic light energy is converted into potential chemical
energy (in the form of high energy bonds of organic “food” compounds) by
photoautotrophs. Energy is again conserved when the high energy bonds of
these “food” molecules are broken and converted to chemical energy
powering the cellular functions of a chemoheterotroph.
D. Metabolic pathways are comprised of a series of reactions. These
pathways must be dynamic and coordinated so that cells can respond to
changes in environment. Each reaction is catalyzed by a specific enzyme.
Every enzyme-catalyzed reaction represents a potential point of regulation
(inhibition or activation). In catabolic pathways the starting compound (an
energy source (food)) is continually oxidized and the electrons are gathered
by electron carrier molecules. The reduced electron carriers represent
ENERGY, as they can drop off their electrons at the electron transport chain
and they can be used to create the proton motive force and ATP (= oxidative
phosphorylation). The energy released from exergonic reactions during
catabolic pathways (e.g. breaking the high energy potential bonds in a food
molecule during glycolysis) can be used to create metabolic intermediates
with high energy, enough to phosphorylate ADP and create ATP =
substrate-level phosphorylation.
Practice: The name given to the reaction involving removal of
electrons or hydrogen atoms from a compound is termed
a. glycolysis
b. reduction
c. oxidation
d. metabolism
[Note - decarboxylation means loss of CO2.]
Some questions may ask you to be able to make a differentiation
between substrate-level and oxidative phosphorylation.
Remember that the phosphorylation of ADP to make ATP
requires energy. If the energy comes from a high-E molecule (e.g.
1,3-BPG) than this is called substrate-level phosphorylation. If,
instead, oxidation of NADH / FADH2 forms the PMF and the
PMF provides the energy to make ATP, this is called oxidative
phosphorylation (OX PHOS).
E. Electron carriers - When reduced, NAD+, FAD and NADP+ all carry 2
electrons. NADH and FADH2 carry their electrons to the electron transport
chain to be used in ATP production. NADPH uses its electrons in anabolic
(biosynthetic) reactions.
Practice: In lecture, we talked about metabolism as we ate donuts. The
glucose molecules in these donuts were gradually oxidized by catabolic
pathways. As the glucose molecules were broken down by oxidation
reactions, electron carrying molecules such as ____________ were reduced.
These electron carrying molecules can then deliver their electrons to the
electron transport chain.
a. NAD+ and FAD
b. ADP and AMP
c. CO2
d. hexokinase
F. ATP (adenosine triphosphate) - UNIVERSAL ENERGY CURRENCY
OF THE CELL!
Practice: The phosphoanhydride bonds of ATP are high in energy because
a. of charge / charge repulsions between the negatively charged
oxygen atoms of the phosphoanhydride groups.
b. the products of hydrolysis are better solvated than ATP itself.
c. the products of hydrolysis are more stable than ATP itself.
d. all of the above
It is not necessary to memorize the structure of ATP, however it is important
to note that ATP has a great deal of potential energy stored in its high energy
phosphoester and phosphoanhydride bonds. When one of these high energy
bonds is broken, a great deal of energy is released (exergonic reaction-, ΔG
is negative). This energy can be used to power endergonic reactions (e.g. the
phosphorylation of glucose in step 1 of glycolysis). When ADP is converted
to ATP by phosphorylation, energy must be invested (endergonic reaction,
ΔG is positive).
Understanding the table of Standard Free Energies of Hydrolysis:
1. The reaction that is third from the bottom in the table is the
hydrolysis of ATP. Looking at the free energy of hydrolysis of ATP
to form ADP, we see that it is an exergonic process that releases 30
kJ/mol (ΔGº’ = -30 kJ/mol). This means that the opposite reaction in
which ATP is phosphorylated is endergonic and requires the input of
30 kJ/mol (ΔGº’ = 30 kJ/mol).
2. Notice that there are many metabolites found above ATP in the
table. For example, the metabolite called phosphoenolpyruvate
(which you’ll recognize as an intermediate in glycolysis), has a free
energy of hydrolysis of -62 kJ/mol. This means that
Phosphoenolpyruvate could very easily and exergonically transfer a
phosphate group to ADP to for ATP. In fact there would be 32 kJ/mol
left over (-62+30 = -32 kJ/mol). This is in fact what happens in step
10 of glycolysis!
3. Also notice that there are some metabolites below ATP on the table,
ATP could easily transfer a phosphoryl group to these metabolites.
For example, ATP could transfer a phosphoryl group to glucose
forming glucose 6-phosphate (in fact, this is the first step of glycolysis
- HOW MUCH ENERGY IS RELEASED WHEN THIS NET
REACTION HAPPENS?).
D. During catabolism, many intermediates are formed. These intermediates
can sometimes be syphoned off and used as building blocks in anabolism.
Intermediates that can be used this way are termed precursor metabolites.