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Exam 2
Metabolism, Biosynthesis, Biodegredation
102
Microbiology
Undergraduate 3
03/11/2013

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Cards

Term
Examples of high energy compounds?
Definition
ATP, UTP, GTP, CTP
Term
How is energy stored in cells?
Definition
ATP
Term
What is the difference between fermentation and respiration?
Definition
The Fate of Pyruvate.

Respiration: completely oxidized to CO2 and Water: most energetically favorable.

Frementaton: it is fermented into an acid or alcohol
Term
Three Possible mechanisms for cells to form ATP?
Definition
Substrate level phosphorylation
Respiration linked phosphorylation
Photo-phosphorylation
Term
Substrate level phosphorylation
Definition
direct transfer of high energy phosphate from phosphoralized organic compound ADP->ATP
Term
Respiration linked phosphorylation
Definition
oxidation of electron donator coupled with reduction of electron acceptor
Term
Photophosphorylation
Definition
Use of light to create a proton motor force.
Term
What is the purpose of each stage of Glycolsis
Definition
phosphorlating everything: preparation

redox stages: energy recovery and production of NADH
Term
What is Gibb's free energy?
Definition
It is the enthalpy of the system-the product of temp(entropy)
Term
How do you determine if a reaction will be favorable or not?
Definition
If delta G is negative the reaction if favorable
Term
What is the role of electron carrier NAD
Definition
it is involved in energy generating catabolic reactions
Term
What is the role of the electron carrier NADP
Definition
it is involved in biosynthesis and anabolic reactions
Term
What is reduction potential
Definition
it is the likelihood that a species will be reduced.
Term
How is reduction potential related to free energy
Definition
The amount of free energy released in a redox reaction is the difference in the redox potential between electron donor and acceptor.
Term
why are Oxiduction-Reduction reactions always coupled
Definition
They can not occur alone
Term
What sort of work can energized membranes (PMF membranes) preform?
Definition
-ATP synthesis
-rotating flagellum
-active membrane transport
Term
What are the 3 characteristics that all electron transport chains must possess?
Definition
-have redox carriers
-create PMF (have alternating electron only and proton &electron carriers)
-they have to be linked to an intact membrane
Term
What is the structure and function of ATP synthase F1 and F0 subunits
Definition
F1 rotates and goes through membrane to inside

F0 sets in the membrane like a pore
Term
Describe the possible fates for energy stored in a photon
Definition
-captured by antenna complex
-transferred to the reaction center
-captured by the reaction center
Term
relation between substrate level phosphorylation and glycolsis
Definition
SLP is a STEP in gylcolsis
Term
What are examples of light gathering systems?
Definition
-Different types of antenna systems
-COMPOSTION OF ANTENNA (ex
caratnoids)
-organization of intracellular membrane complexes
-chlorosomes
- thylicoids
Term
What are dark reactions?
Definition
do not require light.. synthesis processes (ex. Calvin cycle)
Term
What are light reactions?
Definition
Light reactions create ATP
Term
Five types of photosynthetic bacteria compare and contrast
Definition
A: Have ETC
Non-Purple bacteria
Purple Sulfur bacteria
Green sulfur bacteria
cyanobacteria
heliobacteria
*B: Use Rodopsiin
* Heliobacteria
C: Anoxygenic (cyclic photophosphor)
Green Sulfur bacteria
Purple Sulfur Bacteria
Non Purple bacteria
*D: Oxygenic (Z-Scheme)
* Cyanobacteria
*E: Can't use sulfur
*Non purple bacteria
F: Can use sulfur
Purple and Green Sulfur bacteria
*G: Can reduce NADPH
*Green sulfur bacteria
*H: Can not reduce NADPH (use reverse ETC)
*Purple sulfur bacteria
Term
What are the key enzymes in Krebs cycle
Definition
rubisco
Term
Key enzyme in Woods pathway
Definition
carbonmonoxide dehydrogenase
Term
Key enezyme in reverse TCA cycle
Definition
forwards: succinate dehydrogenate
backwards: fumerate reductase
Term
Why is nitrogen fixation so oxygen sensitive?
Definition
it has cofactors that fall apart in presence of oxygen
Term
relationship between ETC and PMF
Definition
ETC produces PMF
Term
what can make a membrane energized?
Definition
-pumping protons out
-ATPase (ATP synthesis backwards)
Term
How does fermentation make ATP
Definition
-through substrate level phosphorylation (do NOT make PMF)
-can make energized membrane with ATPase
Term
How does respiration make ATP
Definition
chemiosmosis
Term
Bacteria with rodopsin do NOT use antenna structure
Definition
Term
Distinguishing enzyme ED
Definition
KDPG aldolase
Term
Distinguishing enzyme Hexose Monophosphate Shunt
Definition
6-phosphogluconate dehydrogenase
Term
distinguishing enzyme of Calvin cycle
Definition
rubisco
Term
Wood Pathway
Definition
carbonmonoxide dehydrogogenase
Term
anaplueric pathways
Definition
replinishes intermediates
Term
What kind of molecules serve as electron acceptors?
Definition
They are molecule or atom that can be reduced by gained an electron from something else.

(they have the most positive reduction potentials)
Term
What kind of molecules are electron donors?
Definition
An electron donor is a molecule or atom that can be oxidized by giving an electron to something else.

They have the most negative reduction potentials.
Term
What determines their role as a donor or acceptor?
Definition
Their relative reduction potentials. The more positive of the two will be the acceptor.
Term
What are electron transport chains?
Definition
ETC's use PMF and are series of electron acceptors and donors that transfer electrons from an electron carrier to a terminal acceptor.
Term
Cofactors associated with the ETC
Definition
NADH: electron carriers

Flavoprotenin: electron and proton carriers

Iron sulfur proteins: electron carriers

Cytochromes: electron carrier

Quinones: carry protons and go to cytochromes
Term
What is the chemiosmotic theory and who proposed it?
Definition
Peter Mitchell proposed the chemiosmotic theory which said that the proton motor force generated by electron transport is employed to drive ATP synthase (enzyme makes ATP from ADP +P)
Term
What are light reactions?
Definition
those that harvest light energy to generate a proton motive force and ATP
Term
What are the four major classes of macromolecules in the bacterial or archaeal cells?
Definition
Proteins, Lipids, Carbohydrates, Nucleic Acids
Term
What is the purpose of precursor metabolites?
Definition
Precursor metabolites are the compounds from which all constituents of the cell can be synthesized.
Term
Precursor molecules of EM Pathway
Definition
glucose-6-phosphate
fructose-6-phosphate
glyceraldehyde-3-phosphate
3-phosphoglycerate
phosphoenolpyruvate
pyruvate
acetyl-CoA
Term
Precursor molecules of the HMS
Definition
Glucose-6-phosphate
ribose-5-phosphate
erythrose-4-phosphate
glyveraldehyde-3-phosphate
pyruvate
acetyl-CoA
Term
Precursor molecules of ED
Definition
glucose-6-phosphate
glyceraldehyde-3-phosphate
pyruvate
acetyl-coA
Term
Precursor molecules of the TCA cycle
Definition
oxaloacetate
alpha-ketogluterate
succinyl-CoA
Term
How are intermediates of the TCA cycle replenished?
Definition
It is an anaplerotic reaction.

through carnoxylation of pyruvate to form oxaloacetate.
Term
What are the other major pathways for CO2 fixation
Definition
Calvin Cycle
Reductive Citric Acid Pathway
Hydeoxypropionate Pathway
Reductive Acetyl-CoA Pathway
Term
What are the molecules that contain nitrogen and what are the relative ease of making biomass from each?
Definition
NO3, NH4, Amino Acids, Organic nitrogen, N2

N2 is used at last resort
Term
What are the two types of nitrate reduction
Definition
Denitroficicaton

assimularoty nitrate reduction pathway
Term
Why is nitrogen fixation a critical microbial process?
Definition
It is because it is essential for all living organisms survival and only microbes can fix N2 gas to a usable form
Term
WHat are the two components of nitrogenase
Definition
FeS
FeMoCo
Term
How much energy is required for nitrogen fixation?
Definition
16 ATP per N2
Term
How can an organism synthesize all of its cell structures from glucose?
Definition
It can because glucose can be used to form all of the precursor molecules which can be used to synthesize any cellular component.
Term
What are the main structural arrangements of proteins
Definition
Primary Structure:
Amino Acids are joined by peptide bonds

Secondary Structure:
Alpha helix
Beta Sheet

Tertiary structure:
many secondary structures together

Quaternary structure:
multiple subunits into a wad
Term
What is the structure and function of the cytoplasmic membrane
Definition
It serves as a primary boundary for the cell's cytoplasm. It is composed of a phospholipid bi layer with proteins inside
Term
How is cell structure and function studied by cell fractionation and separation of components?
Definition
are separated using a centrifuge giving you different layers each with a different cell organelle. the organelle specific layer could be removed and examined more closely giving the scientist the opportunity to understand the purpose and function of the organelle.
Term
How do the position of enexymes and quinones in electron transport chains relate to reduction potential.
Definition
The more negative (higher up) pass to the more positive and the change is the reduction potential.
Term
EM ED and HMS differences
Definition
HMS: produces sugars needed for biosynthesis

ED: only 1 APT produced

EM: uses substrate level phosphorlation more ATP then ED
Term
How is the bacterial cell wall assembled?
Definition
UDP-NAM is synthesized inside the cell and 5 amino acids are added sequentially to form a pentapeptide side chain. Special enzyes are used to add the side chains so tRNA and ribosomes are not involved. It is non UDP-NAM pentapeptide.UDP-NAM is synthesized inside the cell and 5 amino acids are added sequentially to form a pentapeptide side chain. Special enzyes are used to add the side chains so tRNA and ribsobomes are not involved. It is non UDP-NAM pentapeptide.pentapeptide precursor. The completed NAMNAG precursor is transfered across the membrane b the bactoprenol the disachharide pentapeptide is then transfered to the growing end of the peptidoglycan chain outsid the cell. The bactoprenol then reterns inside and loses a phosphate and is ready to repeart the transfer process. The peptide side chains are then linked to eachother using peptide bonds forming crosslinking.
Term
How are flagellae and pili assembled?
Definition
Falgellae:
Assembly begins with synthesis of the MS-ring at the cytoplasm surface. Followed by insertion of proteins composing the basal body including motor shaft proteins and the hook. The addition of motor stator proteins (MOT A and B), The Motor switch protiens and buildup of the filament (FilC subunits). The secretion of proteins across the membrane is done through type III secretion. FilC subunits are transferred through the hollow core of the basal body shaft. hook and growing filament where they self assemble into a helically wound structure.

Pili:
The pilus is assembled from subunits secreted into the periplasm. PapC is assembled first and subunits that are at the tip are assembled first while the ones closest to the cell are assembled last. PapD is a periplasmic chaperone prevents misfolding and premature aggregation of the major and minor subunits of the filaments.
Term
How does bacterial motility function?
Definition
flagella are powered by proton motor force. The energy is used by mot proteins which act as a motor and drives flagellar rotation.
Term
What are the purposes of photosystems I and II in cyanobacteria?
Definition
Photosystem II occurs first and is the sight of photolysis which allows an electron to be boosted to a higher energy level. The passage of this electron to photosystem I drives synthesis of ATP.

Photosystem I: is responsible for reducing NADP+ or providing a reductant that can reduce NADP.
Term
Why does an organism degrade a compound?
Definition
to get energy/food
Term
How does an organism degrade a compound?
Definition
through enzymes
Term
How do we find out if the organism degrades a compound?
Definition
you can use tests for the disappearance of compounds
Term
Why don’t all organisms degrade the compound?
Definition
They don't have the specific enzyme for degradation of that compound.
Term
Van Niel's postulates
Definition
Microbes are present which utilize every constituent part/product as a source of
carbon or energy

Microbes are present in every niche
Term
What is an end product of fermentation?
Definition
Acetate
Term
If a microbe lacked a sufficient iron source, which stage of respiration would be most affected?
Definition
Electron Transport Chain
Term
Which of the following components of the electron chain are freely diffusible in the membrane?
Definition
quinones
Term
According to the chemiosmotic mechanism, ATP is generated when
Definition
protons flow through ATPase.
Term
Which of the following would prevent chemiosmosis from generating ATP?
Definition
All of the Above
Term
Glycolysis has a net yield of _______ molecules of ATP per molecule of glucose consumed.
Definition
2
Term
The usual sequence of redox reactions in aerobic respiration is
Definition
NADH → flavoprotein → nonheme iron protein → CoQ → cytochromes.
Term
The generation of a proton motive force requires
Definition
a closed membrane compartment that is impermeable to protons.
Term
In addition to their ability to harvest light in the 400 to 500 nm range, carotenoids also...
Definition
intercept toxic single-state oxygen.
Term
Photosynthetic halophiles use bacteriorhodopsin...
Definition
to trap light energy and eject protons.
Term
In cyclic phosphorylation, ATP is formed when
Definition
sufficient protons are driven outside the membrane by the cytochrome bc1 complex.
Term
Which of the following can be used as a source of electrons in anoxic photosynthesis?
Definition
both A and B
Term
Antenna pigments can be an advantage to photosynthetic microorganisms because they can
Definition
absorb energy from light of different wavelengths, funneling energy of excitation to reaction centers.
Term
Incorrect
All photosynthetic microorganisms possess all of the following features except
Definition
a capacity for substrate-level phosphorylation.
Term
The characterization of the bacteriorhodopsin system in Halobacterium lent support to
Definition
the chemiosmotic theory of ATP generation.
Term
The thylakoid is a photosynthetic structure characteristic of
Definition
cyanobacteria.
Term
In noncyclic electron flow in nonsulfur purple bacteria, electrons leaving the Q pool
Definition
are used to reduce NAD+.
Term
During cyclic photosynthesis in nonsulfur purple bacteria, which of the following molecules or components acts as both the initial electron donor and the final electron acceptor?
Definition
Bchl 870
Term
There are ______ precursor metabolites that autotrophic bacteria must be able to make from their central metabolic pathways.
Definition
12
Term
In addition to precursor metabolites, what is also produced during the TCA cycle?
Definition
2 CO2, 3 NADHs, 1 FADH2, 1 GTP
Term
Which of these reactions are used to replenish intermediates in central metabolic cycles?
Definition
anaplerotic
Term
The most abundant enzyme on Earth is probably ______.
Definition
rubisco
Term
Acetogenic bacteria produce acetate from ______ by using a key enzyme, acetyl-Co A synthetase/CO dehydrogenase.
Definition
H2 & CO2
Term
The enzyme, GOGAT, is used to replenish ______ when NH4+ is limiting.
Definition
glutamate
Term
For every N2 that is fixed to 2NH3, ______ ATPs are used.
Definition
16
Term
A malonyl-CoA is used per cycle during the biosynthesis of a fatty acid. This adds ______ per cycle.
Definition
2 carbons and releases 1 CO2
Term
Define PMF
Definition
Proton motive force (pmf) is the sum of the membrane electrical potential and the corresponding pH gradient.
Term
What is fermentation?
Definition
Fermentation is defined as the sum of the anaerobic catabolic reactions that provide for the growth of microorganisms when energy is derived solely by substrate-level phosphorylation.
Term
How does photosynthesis
with bactrorodopsin pigment differ from that due to chlorophyll?
Definition
Bacteriorhodopsin can absorb light energy and employ this excitation to carry protons from
the cytoplasm to
the outer surface of the cell, creating a proton motive force. and is a caratnoid structure
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