Microbial Metabalism (BB090) Summary of all lectures
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Course
Microbial Metabolism (BB090)
Institution
Radboud Universiteit Nijmegen (RU)
All the lectures of the course Microbial Metabalism (BB090) given in the 2nd year of the Bachlor Biology. It is mainly picutes and bullet point. Great for people who struggle with large chunks of text.
Lecture 2 BioEnergetics
Anabolism → How the cell build cell components
Catabolism → How the cell converts compounds into
energy
Metabolism - The sum total of all of the chemical
reactions that occur in a cell
● Catabolic reactions (catabolism)
○ Energy-releasing metabolic reactions
○ “Energy metabolism”
● Anabolic reactions (anabolism)
○ Energy-consuming biosynthetic
reactions
○ “Biosynthesis”
Making ATP (energy) is the ultimate goal for all microorganisms.
● Energy required for making ATP comes from chemical reactions
1st law of thermodynamics
Energy can be transformed from one form to
another but not been generated or destroyed
Inorganic chemical metabolism is not found in
eukaryotes
Principles of Bioenergetics
● In any chemical reaction, energy is either
required or released (burn / make).
● Free energy (G): energy released that is
available to do work
● The change in free energy during a reaction is
referred to as ΔG0 ′ (standard conditions)
○ Exergonic: Reactions with –ΔG0 ′ release free energy and can eventually be
used to make ATP.
○ Endergonic: Reactions with +ΔG0 ′ require energy so ATP would be required
to make them work.
,Coupling of endergonic and exergonic reactions
If ΔG0 ′ = 0, the reaction is in equilibrium and nothing happens
● Free-energy calculations do not provide information on reaction rates.
● The reaction rate results from a combination of thermodynamics (G0 ’) and kinetics
(velocity of catalysis)
Catalysis and Enzymes
Catalyst
● Is not being consumed in the reaction
● Lowers the activation energy of a
reaction
● Increases reaction rate
● Does not affect energetics or
equilibrium of a reaction
Enzymes
● Biological catalysts
● Typically proteins (some RNAs)
● Highly specific
● Generally larger than substrate
● Typically rely on weak bonds
○ Examples: hydrogen bonds, van der Waals forces, hydrophobic interactions
● Active site: region of enzyme that binds substrate
Enzyme nomenclature
EC 1. Oxidoreductases
To this class belong all enzymes catalysing oxido-reductions. The substrate oxidized is
regarded as electron donor. Common name is 'dehydrogenase', wherever this is possible; as
an alternative, 'acceptor reductase' can be used.
NADH: ubiquinone oxidoreductase, i.e. NADH dehydrogenase in complex I
,EC 2. Transferases
Transferases are enzymes transferring a group, for example, the methyl group from one
compound (generally regarded as donor) to another compound (generally regarded as
acceptor). The classification is based on the scheme 'donor: acceptor group transferase'.
e.g. CH3 -H4MPT: CoM methyltransferase
EC 3. Hydrolases
These enzymes catalyse the hydrolysis of various bonds.
e.g. peptidase
EC 4. Lyases
Lyases are enzymes cleaving C-C, C-O, C-N and other bonds by other means than by
hydrolysis or oxidation. They differ from other enzymes in that two substrates are involved in
one reaction direction, but only one in the other direction.
e.g. fructose bisphosphate aldolase
EC 5. Isomerases
These enzymes catalyse changes within one molecule.
e.g. triosephosphate isomerase
EC 6. Ligases
Ligases are enzymes that catalyse the joining of two molecules with concomitant hydrolysis
of the diphosphate bond in ATP or a similar triphosphate.
e.g. DNA ligase
Cofactor used in enzyme catalysis
Enzymes therefore make use of cofactors:
● Tighly/covalently bound: prosthetic groups, e.g. Fe-S centers
● Non-covalently bound/ interaction with different enzymes: coenzyme, e.g. NADH)
, Electron donors and acceptors
The standard potential is indicated by E0’(E zero prime)
0 = standard conditions
= 1 mol/L substrate and 1 mol/L product
= 1 atm in the case of gasses
‘ = biological conditions
= pH 7.0, 25 deg centigrade (room temp)
Learning Goals
● Understand and distinguish different types of microbial metabolism and balance
microbiologically relevant redox reactions
● Understand the (bio)chemical principles of microbial metabolism
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