Microbial Metabolism

metabolism

the total of all chemical reactions that occur in the cell

→ catabolism

→ anabolism

catabolism

decrease in molecule’s complexity yielding chemical energy (ATP) for:

→biosynthesis, transport, mechanical work (movement), homeostasis

exergonic reactions: energy out

oxidation or organic and inorganic compounds

→ oxidizing agents: NAD+, FAD+, and O2

Catabolism

decreased complexity

generates energy (ATP)

organic molecule (ex glucose) becomes oxidized ← (something reduced)

if something is oxidized

(loses electrons / H ions) then something is ALWAYS reduced (gains electrons / H ions)

transport

specificity: the ability of an enzyme to discriminate between subtle chemical differences in two similar molecules

affinity: the binding strength involved in ligand-receptor association

→ high affinity: receptor binds ligand even at low ligand concentrations

→ low affinity: receptor binds ligand at high ligand concentration

for every compound a microbe requires for growth, there is at least one transporter dedicated to its uptake

there may be multiple transporters for a single compound but differ in the binding affinity for said compound

gram neg bacteria outermembrane

serves as a selective barrier, only allowing certain molecules to pass through its porins based on size or charge

phosphatidylethanolamine

Forms a bilayer in an aqueous environment

This effectively establishes a barrier through which most molecules cannot pass

special membrane proteins + transporters

→ act as a gate, permitting only certain molecules to pass through the membrane

→ these transporters can be quite specific

→ for all molecules that an organism can metabolize or require for growth, there is a corresponding transporter

cells may have to expand energy to transport some molecules ..

if its concentration in the environment is low

several transport systems have evolved that tie ATP hydrolysis, proton motive force, or solute differential (symporters and antiporters) with the molecule’s uptake

enzymes are catalysts

enzymes lower the activation energy for a chemical reaction to occur at 37 C, pH 7

regulation of metabolic pathways

The flow of carbons through a pathway can be regulated in three major ways:

→ metabolic channeling (Eukaryotes): localization of metabolites and enzymes in different parts of a cell (mitochondria)

→ enzyme activity (Eukaryotes + Bacteria): feedback inhibition, allosteric regulation, covalent modification

→ gene expression (Eukaryotes + Bacteria)

enzymatic control

adaptation to short-term environmental changes

maintain metabolic balance

enzymes

→ are proteins and thus can have different conformations (form). Change in protein form can alter its function or affinity for some substrate

→ enzymatic activity for enzymes associated with rate-limiting step or branch point can be altered in response to the concentration of some end-product associated with that pathway(s)

→ some molecules can act as positive or negative effectors, binding to the enzyme and thus locking it into enzyme active or inactive conformation. Some other enzyme(s) is involved in modifying or removing modifiers from the affected enzyme

Enzymes are catalysts

→ for all reactions that occur in the cell

→ as catalysts, they are not part of the chemical equation

→ enzymes lower the activation energy required for any chemical reaction

→ this allows many of these reactions to occur in the cell at 37 C, pH 7

the 3 stages of catabolism

→ stage 1: large macromolecules are broken down into smaller molecules or subunits. These molecules are transported into the cell where they are further processed and brought into the central catabolic pathways shared by most organisms. The organisms capable of catabolizing these macromolecules have the enzymes and transporters necessary to bring these molecules into central, stage 2 pathways.

→ Stage 2: energy is generated (ATP) from the oxidation of amino acids, sugars, FAs, or glycerol using central pathways common to most organisms (eukaryotes + bacteria)

→ Stage 3: NAD+ and FAD+ are regenerated. The enzymes/pathways behind this are variable among microbes; some use fermentation while others use electron transport and oxidative phosphorylation. Fermentation pathways themselves are viable in their distribution across microbial phyla, orders, and genera. The same is true for electron transport including the donor and receptor molecules that participate in these chemical reaction.

catabolism of glucose

6 carbons to pyruvate (3 carbons)

enzymes (proteins) mediate these chemical reactions

Glycolysis (Embden-Meyerhof)

• Stage 1:

glucose + 2 ATP → Fructose 1,6 diphosphate

commit glucose to glycolysis (aka phosphorylation)

• Stage 2:

Fructose 1,6 diphosphate → 2 glyceraldehyde-3-P

2 glyceraldehyde-3-P → 2 pyruvate (2NADH)

oxidation/reduction step (2NADH)

substrate level phosphorylation

• amphibolic pathway (catabolism/anabolism)

• present in prokaryotes and eukaryotes

TriCarboxylic Acid Cycle (TCA)

Chemical Reactions: Pyruvate, Acetyl CoA, oxidation of NADH and FADH2 by electron transport

Amphibolic pathway: (amphi = “both” = anabolism + catabolism)

→ generation of 6,5, and 4 carbon intermediates for amino acid and heme biosynthesis

→ enzymes are present in prokaryotes and eukaryotes (mitochondria). The TCA cycle, also known as the Krebs cycle, is a series of chemical reactions used by all aerobic organisms to generate energy through the oxidation of acetyl-CoA, producing NADH and FADH2 for the electron transport chain.

electron transport

series of electron carriers that transfer electrons from reductant (ie NADH + H⁺ or FADH2) to final oxidizing agent

Composition of electron transport chain:

→ cytochromes (enzymes with heme cofactor)

→ FeS-proteins (iron-sulfate)

→ coenzymes Q

Asymmetric distribution of electron transport components creates an electrochemical gradient that is used to drive ATP synthesis via chemiosmosis.

cytoplasmic membrane

→ Is central to electron transport/oxidative phosphorylation

→ Enzymes are asymmetrically distributed across the membrane and generate a proton differential from a series of oxidation/reduction steps involving cytochromes, FeS-proteins and CoQ

A proton gate with ATP synthase activity

→ Is capable of converting the chemical potential associated with this proton differential by dissipating the proton gradient and transforming this chemical energy into ATP through oxidative phosphorylation.

NAD+ and FAD+

→ Are recycled using the electron transport chain during cellular respiration, facilitating the transfer of electrons and protons.

respiration vs fermentation

→ respiration is an oxygen-dependent form of catabolism,

→ where fermentation is oxygen-independent

fermentation products

→ are the end products of anaerobic metabolism, including substances like ethanol, lactic acid, and carbon dioxide. (energy sources)

enzymes

→ couple endergonic and exergonic chemical reactions

cells need to synthesize sugars

→ needed to produce glycolipids, glycoproteins, cell walls, capsules, or LPS

→ Can be accomplished through the transformation of glucose

→ If glucose is not available, three steps in glycolysis can be reversed with new enzymes. This is called gluconeogenesis

Nucleosugars (NDP- “sugar”)

→ are key in producing the glycosidic covalent bonds in polysaccharides

→ the hydrolysis of the phosphodiester bond in the NDP-sugar provide the energy needed to make glycosidic bond

synthesis of complex polysaccharides

→ generally require a lipid carrier

→ in bacteria, bactoprenol serves as this carrier for the synthesis of the LPS o-antigen, peptidoglycan, and capsule

nitrogen assimilation

assimilation:

→ anabolic and reductive (NADPH)

→ types: ammonia incorporation (transaminase: a-ketoglutarate, glu and gln), nitrate reduction, nitrogen fixation (some bacteria)

amphibolic pathways

sources for carbon skeleton

→ TCA, glycolysis and pentose-P pathway

transamination reactions

glu or gln are ammonium donors

amino acids recrution

→ recruiting of carbon intermediates from amphibolic pathways or special pathways involved in the synthesis of specific amino acids

anaplerotic reactions

Are required to replenish TCA intermediates drawn off for anabolism

ammonia

→ serves as the nitrogen source in amino acid synthesis

→ this molecule is combined with an a-ketoglutarate to form glutamate

→a 2nd NH4 molecule combines with glutamate to make glutamine

→ glutamine often acts as the nitrogen source in the production of other amino acids

protein synthesis

→ starts with the production of aminoacyl-tRNA, intermediates that translate mRNA sequence into an amino acid sequence

→this costs on ATP for every aminoacyl-tRNA formed

→ one GTP is hydrolyzed to form the 80S ribosome complex on mRNA

→ the equivalent of 3 ATPs are expended for every amino acid into the growing amino acid polypeptide

→ it costs the cell 1,321 ATPs to produce one 330 amino acid polypeptide or protein