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Summary Microbial Physiology, MIB20306, wur
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A summary of Brock Biology of Microorganisms with the relevant chapters for Microbial Physiology, a course given in year 2 of the WUR bachelor Biotechnology.
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Microbial Physiology summaryBy Emma Burgwal wur
Chapter 3
3.1 Macronutrients are required in large amounts, micronutrients in smaller amounts. Some
chemical elements predominate in living systems: C, H, O, N, P, S and Se. About 75% of the net
weight of a microbial cell is water and the remainder are primarily macromolecules (like proteins). All
cells require carbon and nitrogen (ammonia, nitrate) in large amounts and most cells use organic
compounds as their carbon source (breakdown of polymeric substances or direct uptake). Some are
autotroph and get carbon from carbon dioxide.
Microorganisms require metals in small amounts. These are called trace metals and typically function
in the cell as cofactors of enzymes. Growth factors are organic micronutrients, like vitamins. If a cell
needs to grow, it must take up nutrients from its environment.
3.2 Active transport occurs against the concentration gradient. Simple transport is with a single
protein, group translocation with a series of proteins and ABC transport systems consists of three
components: substrate-binding protein, transporter and ATP-hydrolysing protein. They all are
energy-driven. A conformational change opens a protein.
Simple transport: proton motive force (cotransport of proton). These are either a symport or an
antiport.
Group transport: the transport substance is chemically modified during the transport process and an
energy-rich compound drives the transport. The phosphotransferase system phosphorylates
compounds during uptake. Energy comes from an energy-rich intermediate of glycolysis. There are 5
proteins required for this type of transport.
ABC transport system: in the periplasm, catalysed by the activity of periplasmic binding proteins.
These systems catalyse the uptake of a wide variety of (in)organic compounds. They have an
extremely high substrate affinity and the process is driven by ATP.
Although gram-positive bacteria and archaea lack the periplasm, they also have the ABC transport
system. In gram-positive cells this is attached to the external surface of the cytoplasmatic membrane.
3.3 The catabolism is a part of the metabolism and consists of energy-yielding reactions.
Chemotrophs are organisms that conserve energy from chemicals. Chemoorganotrophs use organic
compounds. Chemolithotrophs use inorganic compounds to yield energy. These inorganic
compounds can be oxidized.
Phototrophs contain chlorophylls and other pigments that convert light energy into ATP. Oxygenic
bacteria produce oxygen (cyanobacteria, algae) and anoxygenic photosynthesis produces no oxygen.
Heterotrophs (chemoorganotrophs) get carbon from one or more organic compounds, autotrophs
(most chemolithotrophs) get carbon from carbon dioxide. Autotrophs are primary producers.
In the Calvin Cycle, phototrophs incorporate carbon dioxide into new cell material.
3.4 Energy (in kJ) is the ability to do work. Chemical reactions are accompanied by energy changes,
energy either being required or released. The free energy is the energy available for work. ΔG0 is the
change in free energy where 0 means standard conditions. Exergonic (negative ΔG0) reactions release
energy, endergonic reactions require energy. The free energy of formation (Gf) is the energy
released or required during the formation of a given molecule. This is
zero for elements, for compounds this number differs. Gf is negative
,for exergonic reactions and vice versa. It is possible to calculate ΔG0 by subtracting the sum of the
free energies of formation of the reactants from that of the products. This can only be calculated
once the reaction is balanced.
ΔG is the change in free energy that occurs under the actual conditions. ( ΔG=Δ G 0+ RTlnK ). ΔG
may be more accurate for bioenergetic processes.
Only exergonic reactions yield energy that can be conserved by the cell.
3.5 Free energy says nothing about the rate of a reaction. To break bonds and to start a reaction,
activation energy is required. This is the minimum amount of energy for a reaction to begin. A
catalyst can reduce this energy barrier. This has no effect on energetics or equilibrium. The major
catalysts in cells are enzymes. The enzyme combines with the reactant, the substrate forming an
enzyme-substrate complex. The substrate binds to the active site of the enzyme. Enzymes have
small particles which can be divided in prosthetic groups and coenzymes. Prosthetic groups binds
tightly with covalent bonds and coenzymes are loosely bound.
Endergonic: enzymes convert energy-poor substrates in energy-rich substrates.
Theoretically are all enzymes reversible.
3.6 Reactions that release energy to form ATP require an oxidation-
reduction (=redox) reaction. Oxidation is the removal of an electron,
reduction the gaining of an electron. Redox reactions occur in pairs. It
consists of two half-reactions. The electron donor is the substance to
be oxidized, the electron acceptor the substance to be reduced. Many
substances can be both. A redox couple is the constituents on each
side of the arrow. The reduction potential is the tendency to donate
or accept electrons. The reduced substance is the substance with the
more negative reduction potential.
The redox tower is a convenient way to view electron transfer
reactions, with the strongest donor at the top. The most negative
reactions are at the top. The difference in redox potential is referred
to as ΔE0. The Nernst equation shows a relation between ΔE and ΔG.
In the middle of the redox tower are substance that can accept or
donate electrons.
A common redox coenzyme is NAD. NAD/NADH is an electron plus
proton carrier. These coenzymes increase the redox diversity. It
serves as an intermediate. This electron shuttling of coenzymes is common in microbial catabolism.
3.7 Energy conservation in cells is accomplished through the formation of compounds containing
energy-rich phosphate or sulphur bonds. Phosphate can be bound to organic compounds with ester
or anhydride bonds, however, not all bonds are energy-rich. The most important energy-rich
phosphate compound is ATP. ADP and AMP have less phosphate groups and are thus less energy-
rich. Cells can also use free energy available in the hydrolysis of a handful of energy-rich compounds
such as coenzyme A, because this coenzyme contains thioester bonds. These are important in
anaerobic reactions such as fermentation. For long time storage, microorganisms typically produce
insoluble polymers (granules). Maintenance energy is required to maintain cell integrity (non-
growing state).
3.8 Fermentation is anaerobic catabolism and respiration can be both anaerobic or aerobic. The
glycolysis is a series where glucose can be oxidized to pyruvate, which can be further oxidized to
carbon dioxide. During this reaction, energy-rich compounds are made, which are used for ATP
production by substrate-level phosphorylation. Glycolysis can be divided in three stages.
Stage 1: preparatory reactions. ATP is used here. This stage starts with glucose and ends with two
glyceraldehyde-3-phosphate.
, Stage 2: redox occurs and energy is conserved.
Pyruvate is formed. This stage starts with two
glyceraldehyde-3-phosphate and ends with
pyruvate. Oxidations reactions occur and NAD is
reduced to NADH. Inorganic phosphate is
converted in organic phosphate (first step
energy conservation) for phosphorylation of two
glyceraldehyde-3-phosphate. ATP is than
synthesized. During the first two stages, four
ATP form and two are used.
Stage 3: redox balance achieved and
fermentation products formed. NADH needs to be reoxidized for the next round of glycolysis. This
occurs when pyruvate is reduced to fermentation products. Fermentation by yeast gives carbon
dioxide and ethanol as products, lactic acid bacteria give lactate as product.
Most sugars are fermentable. For fermentation, sugars must be converted in glucose by isomerase
enzymes. The major difference in fermentation processes is in the products. Some bacteria can
produce more energy, when they use coenzyme A for example.
Fermentation is the foundation of baking, beverage industries and key-ingredients in fermented food
(cheese etc). For energy, yeast cells respire glucose rather than ferment it. This is depending on the
oxygen conditions of the environment.
3.9 For respiration, glucose first needs to
be glycolyzed. The pathway where this
oxidation happens is called the citric acid
cycle. Pyruvate is decarboxylated to
acetyl-CoA because of NAD. This can form
citric acid and then a reactions cascade
begins. Two carbon dioxide, one FADH
and four NADH are formed. This cycle
happens two times, because we start with
two pyruvate (out of one glucose). NADH
oxidation yields 3 ATP, FADH oxidation
yields 2 ATP. A total of 38 ATP can be
made after this cycle. Oxaloacetate is an
important intermediate for biosynthesis.
CAC has thus as functions: glucose
respiration coupled to energy conservation and biosynthesis of key metabolites (same as glycolysis).
When oxaloacetate is used for biosynthesis, CAC cannot happen. An alternative will start, the
glyoxylate cycle. This has two additional enzymes and can form malate. This can produce
oxaloacetate.
3.10 Electron transport reactions occur in the membrane. Several types of oxidation-reduction
enzymes participate. These are arranged in order of increasingly more positive reduction potential
(NADH first, cytochrome last). NADH binds and is converted to NAD. The protons and electrons are
passed through to flavoproteins. They pass electrons through. Cytochromes undergo reduction or
oxidation. These occasionally form complexes with other cytochromes. Different iron-sulphur
proteins can function at different locations in the electron transport chain. Cytochromes and iron-
sulphur compounds carry electrons only. Quinones lack a protein component and can therefore
move within the membrane. They work like flavoproteins. They typically link iron-sulphur proteins
and cytochromes.
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